# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading dunbrack-2191.atoms # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 53157 examples # computed average trans backbone unit before proline from 2010 examples # computed average cis backbone unit from 97 examples # trans (non-proline) backbone unit: # CA= -2.2087 1.0126 -0.0030 # O= -0.1499 2.2440 0.0016 # C= -0.6889 1.1368 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 -0.0000 0.0000 # cis backbone unit: # CA= -0.1436 2.4534 -0.0002 # O= -2.0284 0.9742 0.0015 # C= -0.8018 1.0771 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4668 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2100 1.0631 -0.0014 # O= -0.1236 2.2458 0.0075 # C= -0.6872 1.1517 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading dunbrack-2191.atoms have 2191 chains in training database # Count of chains,residues,atoms: 2191,500310,3902258 # 493341 residues have no bad marker # 3226 residues lack atoms needed to compute omega # 1453 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 4 # HAS_OXT 1167 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 3052 # HAS_UNKNOWN_ATOMS 9 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 979 # NON_PLANAR_PEPTIDE 888 # BAD_PEPTIDE 2680 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-2191.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0325/ # command:# Making conformation for sequence T0325 numbered 1 through 262 Created new target T0325 from T0325.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0325/ # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0325/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0325/decoys/ # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS4.pdb.gz looking for model 1 # choosing archetypes in rotamer library # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS5 # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # Found a chain break before 222 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS1 # ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1 # Found a chain break before 204 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS2 # ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1 # Found a chain break before 198 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS3 # ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1 # Found a chain break before 190 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS4 # ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1 # Found a chain break before 210 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS5 # ReadConformPDB reading from PDB file servers/ABIpro_TS1.pdb.gz looking for model 1 # Found a chain break before 254 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS1 # ReadConformPDB reading from PDB file servers/ABIpro_TS2.pdb.gz looking for model 1 # Found a chain break before 254 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS2 # ReadConformPDB reading from PDB file servers/ABIpro_TS3.pdb.gz looking for model 1 # Found a chain break before 245 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS3 # ReadConformPDB reading from PDB file servers/ABIpro_TS4.pdb.gz looking for model 1 # Found a chain break before 240 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS4 # ReadConformPDB reading from PDB file servers/ABIpro_TS5.pdb.gz looking for model 1 # Found a chain break before 209 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1 # Found a chain break before 236 # copying to AlignedFragments data structure # naming current conformation BayesHH_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1 # naming current conformation Bilab-ENABLE_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS2.pdb.gz looking for model 1 # naming current conformation Bilab-ENABLE_TS2 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS3.pdb.gz looking for model 1 # naming current conformation Bilab-ENABLE_TS3 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS4.pdb.gz looking for model 1 # naming current conformation Bilab-ENABLE_TS4 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS5.pdb.gz looking for model 1 # Found a chain break before 178 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS5 # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # Found a chain break before 238 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS3 # ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1 # Found a chain break before 256 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS4 # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS5 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS2 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS3 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS4 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS5 # ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation Distill_TS1 # ReadConformPDB reading from PDB file servers/Distill_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation Distill_TS2 # ReadConformPDB reading from PDB file servers/Distill_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation Distill_TS3 # ReadConformPDB reading from PDB file servers/Distill_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation Distill_TS4 # ReadConformPDB reading from PDB file servers/Distill_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation Distill_TS5 # ReadConformPDB reading from PDB file servers/FAMSD_TS1.pdb.gz looking for model 1 # Found a chain break before 258 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS1 # ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation FAMSD_TS2 # ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1 # Found a chain break before 260 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS3 # ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1 # Found a chain break before 261 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS4 # ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation FAMSD_TS5 # ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1 # Found a chain break before 255 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation FAMS_TS3 # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation FAMS_TS4 # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # Found a chain break before 256 # copying to AlignedFragments data structure # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # Found a chain break before 216 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS1 # ReadConformPDB reading from PDB file servers/FOLDpro_TS2.pdb.gz looking for model 1 # Found a chain break before 228 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS2 # ReadConformPDB reading from PDB file servers/FOLDpro_TS3.pdb.gz looking for model 1 # Found a chain break before 160 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS3 # ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1 # Found a chain break before 156 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS4 # ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1 # Found a chain break before 166 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS5 # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation FORTE1_AL1 # ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation FORTE1_AL2 # ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation FORTE1_AL3 # ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation FORTE1_AL4 # ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1 Skipped atom 149, because occupancy 1 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz Skipped atom 150, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz Skipped atom 151, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz Skipped atom 152, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz Skipped atom 545, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz Skipped atom 546, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz Skipped atom 547, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz Skipped atom 548, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation FORTE1_AL5 # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation FORTE2_AL1 # ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation FORTE2_AL2 # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation FORTE2_AL3 # ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation FORTE2_AL4 # ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation FORTE2_AL5 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS1.pdb.gz looking for model 1 # Found a chain break before 233 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS1 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS2.pdb.gz looking for model 1 # Found a chain break before 260 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS2 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS3.pdb.gz looking for model 1 # Found a chain break before 182 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS3 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS4.pdb.gz looking for model 1 # Found a chain break before 257 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS4 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS5.pdb.gz looking for model 1 # Found a chain break before 261 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS5 # ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # Found a chain break before 227 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS2 # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS3 # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS4 # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS5 # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation FUGUE_AL1 # ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation FUGUE_AL3 # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation FUGUE_AL4 # ReadConformPDB reading from PDB file servers/FUGUE_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation FUGUE_AL5 # ReadConformPDB reading from PDB file servers/FUNCTION_TS1.pdb.gz looking for model 1 # Found a chain break before 255 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS1 # ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1 # Found a chain break before 258 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS2 # ReadConformPDB reading from PDB file servers/FUNCTION_TS3.pdb.gz looking for model 1 # Found a chain break before 258 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS3 # ReadConformPDB reading from PDB file servers/FUNCTION_TS4.pdb.gz looking for model 1 # Found a chain break before 261 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS4 # ReadConformPDB reading from PDB file servers/FUNCTION_TS5.pdb.gz looking for model 1 # Found a chain break before 238 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # Found a chain break before 241 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS1 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # Found a chain break before 189 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # Found a chain break before 187 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS3 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS4 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS5 # ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1 # Found a chain break before 189 # copying to AlignedFragments data structure # naming current conformation HHpred1_TS1 # ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1 # Found a chain break before 190 # copying to AlignedFragments data structure # naming current conformation HHpred2_TS1 # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 # Found a chain break before 176 # copying to AlignedFragments data structure # naming current conformation HHpred3_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS2 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS3 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS4 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS5 # ReadConformPDB reading from PDB file servers/LOOPP_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation LOOPP_TS1 # ReadConformPDB reading from PDB file servers/LOOPP_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation LOOPP_TS2 # ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation LOOPP_TS3 # ReadConformPDB reading from PDB file servers/LOOPP_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation LOOPP_TS4 # ReadConformPDB reading from PDB file servers/LOOPP_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation LOOPP_TS5 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS1.pdb.gz looking for model 1 # Found a chain break before 257 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS2.pdb.gz looking for model 1 # Found a chain break before 200 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS3.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS4.pdb.gz looking for model 1 # Found a chain break before 217 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS5.pdb.gz looking for model 1 # Found a chain break before 259 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS5 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # Found a chain break before 259 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS2.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS3.pdb.gz looking for model 1 # Found a chain break before 251 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS4.pdb.gz looking for model 1 # Found a chain break before 156 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS5.pdb.gz looking for model 1 # Found a chain break before 257 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS5 # ReadConformPDB reading from PDB file servers/MetaTasser_TS1.pdb.gz looking for model 1 # Found a chain break before 254 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS1 # ReadConformPDB reading from PDB file servers/MetaTasser_TS2.pdb.gz looking for model 1 # Found a chain break before 260 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS2 # ReadConformPDB reading from PDB file servers/MetaTasser_TS3.pdb.gz looking for model 1 # Found a chain break before 261 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS3 # ReadConformPDB reading from PDB file servers/MetaTasser_TS4.pdb.gz looking for model 1 # Found a chain break before 261 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS4 # ReadConformPDB reading from PDB file servers/MetaTasser_TS5.pdb.gz looking for model 1 # Found a chain break before 254 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS5 # ReadConformPDB reading from PDB file servers/NN_PUT_lab_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation NN_PUT_lab_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS1.pdb.gz looking for model 1 # Found a chain break before 257 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS2.pdb.gz looking for model 1 # Found a chain break before 254 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS2 # ReadConformPDB reading from PDB file servers/POMYSL_TS3.pdb.gz looking for model 1 # Found a chain break before 250 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS3 # ReadConformPDB reading from PDB file servers/POMYSL_TS4.pdb.gz looking for model 1 # Found a chain break before 258 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS4 # ReadConformPDB reading from PDB file servers/POMYSL_TS5.pdb.gz looking for model 1 # Found a chain break before 256 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1 # Found a chain break before 236 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # Found a chain break before 232 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # Found a chain break before 241 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # Found a chain break before 232 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # Found a chain break before 238 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS5 # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation Pcons6_TS1 # ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation Pcons6_TS2 # ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation Pcons6_TS3 # ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation Pcons6_TS4 # ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation Pcons6_TS5 # ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation Phyre-1_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation Phyre-2_TS2 # ReadConformPDB reading from PDB file servers/Phyre-2_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation Phyre-2_TS3 # ReadConformPDB reading from PDB file servers/Phyre-2_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation Phyre-2_TS4 # ReadConformPDB reading from PDB file servers/Phyre-2_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS5 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS1 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS2 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # Found a chain break before 237 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS3 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # Found a chain break before 211 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS4 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1 # Found a chain break before 238 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1 # Found a chain break before 228 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1 # Found a chain break before 223 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1 # Found a chain break before 225 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS4.pdb.gz looking for model 1 # Found a chain break before 261 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1 # Found a chain break before 44 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS5 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS1.pdb.gz looking for model 1 # Found a chain break before 176 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS1 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1 # Found a chain break before 258 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS2 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS3.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS3 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS4.pdb.gz looking for model 1 # Found a chain break before 258 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS4 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS5.pdb.gz looking for model 1 # Found a chain break before 229 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR_TS1.pdb.gz looking for model 1 # Found a chain break before 187 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1 # Found a chain break before 251 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR_TS3.pdb.gz looking for model 1 Faking rotamer for incomplete or colinear backbone at (T0325)N107 Faking rotamer for incomplete or colinear backbone at (T0325)N107 # Found a chain break before 258 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR_TS4.pdb.gz looking for model 1 # Found a chain break before 208 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1 # Found a chain break before 154 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS5 # ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1 # Found a chain break before 238 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS1 # ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1 # Found a chain break before 239 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS2 # ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1 # Found a chain break before 237 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS3 # ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1 # Found a chain break before 211 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS4 # ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1 # Found a chain break before 241 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS5 # ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1 WARNING: atoms too close: (T0325)N9.CA and (T0325)N9.CB only 0.000 apart, marking (T0325)N9.CB as missing WARNING: atoms too close: (T0325)V19.CA and (T0325)V19.CB only 0.000 apart, marking (T0325)V19.CB as missing WARNING: atoms too close: (T0325)E25.CA and (T0325)E25.CB only 0.000 apart, marking (T0325)E25.CB as missing WARNING: atoms too close: (T0325)T40.CA and (T0325)T40.CB only 0.000 apart, marking (T0325)T40.CB as missing WARNING: atoms too close: (T0325)Y43.CA and (T0325)Y43.CB only 0.000 apart, marking (T0325)Y43.CB as missing WARNING: atoms too close: (T0325)P73.CA and (T0325)P73.CB only 0.000 apart, marking (T0325)P73.CB as missing WARNING: atoms too close: (T0325)R77.CA and (T0325)R77.CB only 0.000 apart, marking (T0325)R77.CB as missing WARNING: atoms too close: (T0325)V80.CA and (T0325)V80.CB only 0.000 apart, marking (T0325)V80.CB as missing WARNING: atoms too close: (T0325)D85.CA and (T0325)D85.CB only 0.000 apart, marking (T0325)D85.CB as missing WARNING: atoms too close: (T0325)A87.CA and (T0325)A87.CB only 0.000 apart, marking (T0325)A87.CB as missing WARNING: atoms too close: (T0325)F90.CA and (T0325)F90.CB only 0.000 apart, marking (T0325)F90.CB as missing WARNING: atoms too close: (T0325)S94.CA and (T0325)S94.CB only 0.000 apart, marking (T0325)S94.CB as missing WARNING: atoms too close: (T0325)E97.CA and (T0325)E97.CB only 0.000 apart, marking (T0325)E97.CB as missing WARNING: atoms too close: (T0325)E103.CA and (T0325)E103.CB only 0.000 apart, marking (T0325)E103.CB as missing WARNING: atoms too close: (T0325)E108.CA and (T0325)E108.CB only 0.000 apart, marking (T0325)E108.CB as missing WARNING: atoms too close: (T0325)I114.CA and (T0325)I114.CB only 0.000 apart, marking (T0325)I114.CB as missing WARNING: atoms too close: (T0325)D124.CA and (T0325)D124.CB only 0.000 apart, marking (T0325)D124.CB as missing WARNING: atoms too close: (T0325)V132.CA and (T0325)V132.CB only 0.000 apart, marking (T0325)V132.CB as missing WARNING: atoms too close: (T0325)A147.CA and (T0325)A147.CB only 0.000 apart, marking (T0325)A147.CB as missing WARNING: atoms too close: (T0325)Y150.CA and (T0325)Y150.CB only 0.000 apart, marking (T0325)Y150.CB as missing WARNING: atoms too close: (T0325)S160.CA and (T0325)S160.CB only 0.000 apart, marking (T0325)S160.CB as missing WARNING: atoms too close: (T0325)T163.CA and (T0325)T163.CB only 0.000 apart, marking (T0325)T163.CB as missing WARNING: atoms too close: (T0325)Y166.CA and (T0325)Y166.CB only 0.000 apart, marking (T0325)Y166.CB as missing WARNING: atoms too close: (T0325)L169.CA and (T0325)L169.CB only 0.000 apart, marking (T0325)L169.CB as missing WARNING: atoms too close: (T0325)Q171.CA and (T0325)Q171.CB only 0.000 apart, marking (T0325)Q171.CB as missing WARNING: atoms too close: (T0325)K186.CA and (T0325)K186.CB only 0.000 apart, marking (T0325)K186.CB as missing WARNING: atoms too close: (T0325)T192.CA and (T0325)T192.CB only 0.000 apart, marking (T0325)T192.CB as missing WARNING: atoms too close: (T0325)I193.CA and (T0325)I193.CB only 0.000 apart, marking (T0325)I193.CB as missing WARNING: atoms too close: (T0325)M199.CA and (T0325)M199.CB only 0.000 apart, marking (T0325)M199.CB as missing WARNING: atoms too close: (T0325)E209.CA and (T0325)E209.CB only 0.000 apart, marking (T0325)E209.CB as missing WARNING: atoms too close: (T0325)C228.CA and (T0325)C228.CB only 0.000 apart, marking (T0325)C228.CB as missing WARNING: atoms too close: (T0325)E236.CA and (T0325)E236.CB only 0.000 apart, marking (T0325)E236.CB as missing WARNING: atoms too close: (T0325)S259.CA and (T0325)S259.CB only 0.000 apart, marking (T0325)S259.CB as missing # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS1 # ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1 WARNING: atoms too close: (T0325)K4.CA and (T0325)K4.CB only 0.000 apart, marking (T0325)K4.CB as missing WARNING: atoms too close: (T0325)Y15.CA and (T0325)Y15.CB only 0.000 apart, marking (T0325)Y15.CB as missing WARNING: atoms too close: (T0325)I23.CA and (T0325)I23.CB only 0.000 apart, marking (T0325)I23.CB as missing WARNING: atoms too close: (T0325)L38.CA and (T0325)L38.CB only 0.000 apart, marking (T0325)L38.CB as missing WARNING: atoms too close: (T0325)Y43.CA and (T0325)Y43.CB only 0.000 apart, marking (T0325)Y43.CB as missing WARNING: atoms too close: (T0325)A51.CA and (T0325)A51.CB only 0.000 apart, marking (T0325)A51.CB as missing WARNING: atoms too close: (T0325)R52.CA and (T0325)R52.CB only 0.000 apart, marking (T0325)R52.CB as missing WARNING: atoms too close: (T0325)A59.CA and (T0325)A59.CB only 0.000 apart, marking (T0325)A59.CB as missing WARNING: atoms too close: (T0325)I60.CA and (T0325)I60.CB only 0.000 apart, marking (T0325)I60.CB as missing WARNING: atoms too close: (T0325)P73.CA and (T0325)P73.CB only 0.000 apart, marking (T0325)P73.CB as missing WARNING: atoms too close: (T0325)E78.CA and (T0325)E78.CB only 0.000 apart, marking (T0325)E78.CB as missing WARNING: atoms too close: (T0325)V80.CA and (T0325)V80.CB only 0.000 apart, marking (T0325)V80.CB as missing WARNING: atoms too close: (T0325)P81.CA and (T0325)P81.CB only 0.000 apart, marking (T0325)P81.CB as missing WARNING: atoms too close: (T0325)D85.CA and (T0325)D85.CB only 0.000 apart, marking (T0325)D85.CB as missing WARNING: atoms too close: (T0325)Y89.CA and (T0325)Y89.CB only 0.000 apart, marking (T0325)Y89.CB as missing WARNING: atoms too close: (T0325)E97.CA and (T0325)E97.CB only 0.000 apart, marking (T0325)E97.CB as missing WARNING: atoms too close: (T0325)I114.CA and (T0325)I114.CB only 0.000 apart, marking (T0325)I114.CB as missing WARNING: atoms too close: (T0325)M117.CA and (T0325)M117.CB only 0.000 apart, marking (T0325)M117.CB as missing WARNING: atoms too close: (T0325)D124.CA and (T0325)D124.CB only 0.000 apart, marking (T0325)D124.CB as missing WARNING: atoms too close: (T0325)R148.CA and (T0325)R148.CB only 0.000 apart, marking (T0325)R148.CB as missing WARNING: atoms too close: (T0325)Y150.CA and (T0325)Y150.CB only 0.000 apart, marking (T0325)Y150.CB as missing WARNING: atoms too close: (T0325)L154.CA and (T0325)L154.CB only 0.000 apart, marking (T0325)L154.CB as missing WARNING: atoms too close: (T0325)R155.CA and (T0325)R155.CB only 0.000 apart, marking (T0325)R155.CB as missing WARNING: atoms too close: (T0325)S158.CA and (T0325)S158.CB only 0.000 apart, marking (T0325)S158.CB as missing WARNING: atoms too close: (T0325)K164.CA and (T0325)K164.CB only 0.000 apart, marking (T0325)K164.CB as missing WARNING: atoms too close: (T0325)V173.CA and (T0325)V173.CB only 0.000 apart, marking (T0325)V173.CB as missing WARNING: atoms too close: (T0325)Y184.CA and (T0325)Y184.CB only 0.000 apart, marking (T0325)Y184.CB as missing WARNING: atoms too close: (T0325)I193.CA and (T0325)I193.CB only 0.000 apart, marking (T0325)I193.CB as missing WARNING: atoms too close: (T0325)L194.CA and (T0325)L194.CB only 0.000 apart, marking (T0325)L194.CB as missing WARNING: atoms too close: (T0325)Q222.CA and (T0325)Q222.CB only 0.000 apart, marking (T0325)Q222.CB as missing WARNING: atoms too close: (T0325)C228.CA and (T0325)C228.CB only 0.000 apart, marking (T0325)C228.CB as missing WARNING: atoms too close: (T0325)E236.CA and (T0325)E236.CB only 0.000 apart, marking (T0325)E236.CB as missing WARNING: atoms too close: (T0325)Q241.CA and (T0325)Q241.CB only 0.000 apart, marking (T0325)Q241.CB as missing WARNING: atoms too close: (T0325)K244.CA and (T0325)K244.CB only 0.000 apart, marking (T0325)K244.CB as missing WARNING: atoms too close: (T0325)E249.CA and (T0325)E249.CB only 0.000 apart, marking (T0325)E249.CB as missing WARNING: atoms too close: (T0325)L253.CA and (T0325)L253.CB only 0.000 apart, marking (T0325)L253.CB as missing WARNING: atoms too close: (T0325)M262.CA and (T0325)M262.CB only 0.000 apart, marking (T0325)M262.CB as missing # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS2 # ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1 WARNING: atoms too close: (T0325)S2.CA and (T0325)S2.CB only 0.000 apart, marking (T0325)S2.CB as missing WARNING: atoms too close: (T0325)I7.CA and (T0325)I7.CB only 0.000 apart, marking (T0325)I7.CB as missing WARNING: atoms too close: (T0325)D11.CA and (T0325)D11.CB only 0.000 apart, marking (T0325)D11.CB as missing WARNING: atoms too close: (T0325)F13.CA and (T0325)F13.CB only 0.000 apart, marking (T0325)F13.CB as missing WARNING: atoms too close: (T0325)Q21.CA and (T0325)Q21.CB only 0.000 apart, marking (T0325)Q21.CB as missing WARNING: atoms too close: (T0325)L38.CA and (T0325)L38.CB only 0.000 apart, marking (T0325)L38.CB as missing WARNING: atoms too close: (T0325)T40.CA and (T0325)T40.CB only 0.000 apart, marking (T0325)T40.CB as missing WARNING: atoms too close: (T0325)S41.CA and (T0325)S41.CB only 0.000 apart, marking (T0325)S41.CB as missing WARNING: atoms too close: (T0325)P56.CA and (T0325)P56.CB only 0.000 apart, marking (T0325)P56.CB as missing WARNING: atoms too close: (T0325)T65.CA and (T0325)T65.CB only 0.000 apart, marking (T0325)T65.CB as missing WARNING: atoms too close: (T0325)S82.CA and (T0325)S82.CB only 0.000 apart, marking (T0325)S82.CB as missing WARNING: atoms too close: (T0325)V84.CA and (T0325)V84.CB only 0.000 apart, marking (T0325)V84.CB as missing WARNING: atoms too close: (T0325)F90.CA and (T0325)F90.CB only 0.000 apart, marking (T0325)F90.CB as missing WARNING: atoms too close: (T0325)V105.CA and (T0325)V105.CB only 0.000 apart, marking (T0325)V105.CB as missing WARNING: atoms too close: (T0325)I114.CA and (T0325)I114.CB only 0.000 apart, marking (T0325)I114.CB as missing WARNING: atoms too close: (T0325)H125.CA and (T0325)H125.CB only 0.000 apart, marking (T0325)H125.CB as missing WARNING: atoms too close: (T0325)D127.CA and (T0325)D127.CB only 0.000 apart, marking (T0325)D127.CB as missing WARNING: atoms too close: (T0325)K138.CA and (T0325)K138.CB only 0.000 apart, marking (T0325)K138.CB as missing WARNING: atoms too close: (T0325)A147.CA and (T0325)A147.CB only 0.000 apart, marking (T0325)A147.CB as missing WARNING: atoms too close: (T0325)K149.CA and (T0325)K149.CB only 0.000 apart, marking (T0325)K149.CB as missing WARNING: atoms too close: (T0325)Y150.CA and (T0325)Y150.CB only 0.000 apart, marking (T0325)Y150.CB as missing WARNING: atoms too close: (T0325)K164.CA and (T0325)K164.CB only 0.000 apart, marking (T0325)K164.CB as missing WARNING: atoms too close: (T0325)Q171.CA and (T0325)Q171.CB only 0.000 apart, marking (T0325)Q171.CB as missing WARNING: atoms too close: (T0325)K186.CA and (T0325)K186.CB only 0.000 apart, marking (T0325)K186.CB as missing WARNING: atoms too close: (T0325)I188.CA and (T0325)I188.CB only 0.000 apart, marking (T0325)I188.CB as missing WARNING: atoms too close: (T0325)T190.CA and (T0325)T190.CB only 0.000 apart, marking (T0325)T190.CB as missing WARNING: atoms too close: (T0325)L194.CA and (T0325)L194.CB only 0.000 apart, marking (T0325)L194.CB as missing WARNING: atoms too close: (T0325)L196.CA and (T0325)L196.CB only 0.000 apart, marking (T0325)L196.CB as missing WARNING: atoms too close: (T0325)I210.CA and (T0325)I210.CB only 0.000 apart, marking (T0325)I210.CB as missing WARNING: atoms too close: (T0325)R231.CA and (T0325)R231.CB only 0.000 apart, marking (T0325)R231.CB as missing WARNING: atoms too close: (T0325)L238.CA and (T0325)L238.CB only 0.000 apart, marking (T0325)L238.CB as missing WARNING: atoms too close: (T0325)R250.CA and (T0325)R250.CB only 0.000 apart, marking (T0325)R250.CB as missing WARNING: atoms too close: (T0325)L253.CA and (T0325)L253.CB only 0.000 apart, marking (T0325)L253.CB as missing WARNING: atoms too close: (T0325)A255.CA and (T0325)A255.CB only 0.000 apart, marking (T0325)A255.CB as missing WARNING: atoms too close: (T0325)S259.CA and (T0325)S259.CB only 0.000 apart, marking (T0325)S259.CB as missing WARNING: atoms too close: (T0325)M262.CA and (T0325)M262.CB only 0.000 apart, marking (T0325)M262.CB as missing # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS3 # ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1 WARNING: atoms too close: (T0325)M1.CA and (T0325)M1.CB only 0.000 apart, marking (T0325)M1.CB as missing WARNING: atoms too close: (T0325)K4.CA and (T0325)K4.CB only 0.000 apart, marking (T0325)K4.CB as missing WARNING: atoms too close: (T0325)I24.CA and (T0325)I24.CB only 0.000 apart, marking (T0325)I24.CB as missing WARNING: atoms too close: (T0325)Y43.CA and (T0325)Y43.CB only 0.000 apart, marking (T0325)Y43.CB as missing WARNING: atoms too close: (T0325)R52.CA and (T0325)R52.CB only 0.000 apart, marking (T0325)R52.CB as missing WARNING: atoms too close: (T0325)P56.CA and (T0325)P56.CB only 0.000 apart, marking (T0325)P56.CB as missing WARNING: atoms too close: (T0325)L58.CA and (T0325)L58.CB only 0.000 apart, marking (T0325)L58.CB as missing WARNING: atoms too close: (T0325)A59.CA and (T0325)A59.CB only 0.000 apart, marking (T0325)A59.CB as missing WARNING: atoms too close: (T0325)I60.CA and (T0325)I60.CB only 0.000 apart, marking (T0325)I60.CB as missing WARNING: atoms too close: (T0325)T65.CA and (T0325)T65.CB only 0.000 apart, marking (T0325)T65.CB as missing WARNING: atoms too close: (T0325)R77.CA and (T0325)R77.CB only 0.000 apart, marking (T0325)R77.CB as missing WARNING: atoms too close: (T0325)E97.CA and (T0325)E97.CB only 0.000 apart, marking (T0325)E97.CB as missing WARNING: atoms too close: (T0325)N101.CA and (T0325)N101.CB only 0.000 apart, marking (T0325)N101.CB as missing WARNING: atoms too close: (T0325)I113.CA and (T0325)I113.CB only 0.000 apart, marking (T0325)I113.CB as missing WARNING: atoms too close: (T0325)F116.CA and (T0325)F116.CB only 0.000 apart, marking (T0325)F116.CB as missing WARNING: atoms too close: (T0325)M117.CA and (T0325)M117.CB only 0.000 apart, marking (T0325)M117.CB as missing WARNING: atoms too close: (T0325)R122.CA and (T0325)R122.CB only 0.000 apart, marking (T0325)R122.CB as missing WARNING: atoms too close: (T0325)D124.CA and (T0325)D124.CB only 0.000 apart, marking (T0325)D124.CB as missing WARNING: atoms too close: (T0325)H129.CA and (T0325)H129.CB only 0.000 apart, marking (T0325)H129.CB as missing WARNING: atoms too close: (T0325)A145.CA and (T0325)A145.CB only 0.000 apart, marking (T0325)A145.CB as missing WARNING: atoms too close: (T0325)L146.CA and (T0325)L146.CB only 0.000 apart, marking (T0325)L146.CB as missing WARNING: atoms too close: (T0325)K149.CA and (T0325)K149.CB only 0.000 apart, marking (T0325)K149.CB as missing WARNING: atoms too close: (T0325)Y150.CA and (T0325)Y150.CB only 0.000 apart, marking (T0325)Y150.CB as missing WARNING: atoms too close: (T0325)T163.CA and (T0325)T163.CB only 0.000 apart, marking (T0325)T163.CB as missing WARNING: atoms too close: (T0325)D177.CA and (T0325)D177.CB only 0.000 apart, marking (T0325)D177.CB as missing WARNING: atoms too close: (T0325)K186.CA and (T0325)K186.CB only 0.000 apart, marking (T0325)K186.CB as missing WARNING: atoms too close: (T0325)I193.CA and (T0325)I193.CB only 0.000 apart, marking (T0325)I193.CB as missing WARNING: atoms too close: (T0325)L197.CA and (T0325)L197.CB only 0.000 apart, marking (T0325)L197.CB as missing WARNING: atoms too close: (T0325)S203.CA and (T0325)S203.CB only 0.000 apart, marking (T0325)S203.CB as missing WARNING: atoms too close: (T0325)V207.CA and (T0325)V207.CB only 0.000 apart, marking (T0325)V207.CB as missing WARNING: atoms too close: (T0325)C212.CA and (T0325)C212.CB only 0.000 apart, marking (T0325)C212.CB as missing WARNING: atoms too close: (T0325)H213.CA and (T0325)H213.CB only 0.000 apart, marking (T0325)H213.CB as missing WARNING: atoms too close: (T0325)N223.CA and (T0325)N223.CB only 0.000 apart, marking (T0325)N223.CB as missing WARNING: atoms too close: (T0325)S225.CA and (T0325)S225.CB only 0.000 apart, marking (T0325)S225.CB as missing WARNING: atoms too close: (T0325)L238.CA and (T0325)L238.CB only 0.000 apart, marking (T0325)L238.CB as missing WARNING: atoms too close: (T0325)L253.CA and (T0325)L253.CB only 0.000 apart, marking (T0325)L253.CB as missing WARNING: atoms too close: (T0325)A255.CA and (T0325)A255.CB only 0.000 apart, marking (T0325)A255.CB as missing WARNING: atoms too close: (T0325)S259.CA and (T0325)S259.CB only 0.000 apart, marking (T0325)S259.CB as missing # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS4 # ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1 WARNING: atoms too close: (T0325)S2.CA and (T0325)S2.CB only 0.000 apart, marking (T0325)S2.CB as missing WARNING: atoms too close: (T0325)N9.CA and (T0325)N9.CB only 0.000 apart, marking (T0325)N9.CB as missing WARNING: atoms too close: (T0325)Q21.CA and (T0325)Q21.CB only 0.000 apart, marking (T0325)Q21.CB as missing WARNING: atoms too close: (T0325)I24.CA and (T0325)I24.CB only 0.000 apart, marking (T0325)I24.CB as missing WARNING: atoms too close: (T0325)M48.CA and (T0325)M48.CB only 0.000 apart, marking (T0325)M48.CB as missing WARNING: atoms too close: (T0325)A51.CA and (T0325)A51.CB only 0.000 apart, marking (T0325)A51.CB as missing WARNING: atoms too close: (T0325)A55.CA and (T0325)A55.CB only 0.000 apart, marking (T0325)A55.CB as missing WARNING: atoms too close: (T0325)L58.CA and (T0325)L58.CB only 0.000 apart, marking (T0325)L58.CB as missing WARNING: atoms too close: (T0325)I60.CA and (T0325)I60.CB only 0.000 apart, marking (T0325)I60.CB as missing WARNING: atoms too close: (T0325)L64.CA and (T0325)L64.CB only 0.000 apart, marking (T0325)L64.CB as missing WARNING: atoms too close: (T0325)Q70.CA and (T0325)Q70.CB only 0.000 apart, marking (T0325)Q70.CB as missing WARNING: atoms too close: (T0325)K72.CA and (T0325)K72.CB only 0.000 apart, marking (T0325)K72.CB as missing WARNING: atoms too close: (T0325)M79.CA and (T0325)M79.CB only 0.000 apart, marking (T0325)M79.CB as missing WARNING: atoms too close: (T0325)A87.CA and (T0325)A87.CB only 0.000 apart, marking (T0325)A87.CB as missing WARNING: atoms too close: (T0325)F90.CA and (T0325)F90.CB only 0.000 apart, marking (T0325)F90.CB as missing WARNING: atoms too close: (T0325)V100.CA and (T0325)V100.CB only 0.000 apart, marking (T0325)V100.CB as missing WARNING: atoms too close: (T0325)N101.CA and (T0325)N101.CB only 0.000 apart, marking (T0325)N101.CB as missing WARNING: atoms too close: (T0325)V105.CA and (T0325)V105.CB only 0.000 apart, marking (T0325)V105.CB as missing WARNING: atoms too close: (T0325)H125.CA and (T0325)H125.CB only 0.000 apart, marking (T0325)H125.CB as missing WARNING: atoms too close: (T0325)H130.CA and (T0325)H130.CB only 0.000 apart, marking (T0325)H130.CB as missing WARNING: atoms too close: (T0325)K149.CA and (T0325)K149.CB only 0.000 apart, marking (T0325)K149.CB as missing WARNING: atoms too close: (T0325)L152.CA and (T0325)L152.CB only 0.000 apart, marking (T0325)L152.CB as missing WARNING: atoms too close: (T0325)A157.CA and (T0325)A157.CB only 0.000 apart, marking (T0325)A157.CB as missing WARNING: atoms too close: (T0325)L169.CA and (T0325)L169.CB only 0.000 apart, marking (T0325)L169.CB as missing WARNING: atoms too close: (T0325)Q171.CA and (T0325)Q171.CB only 0.000 apart, marking (T0325)Q171.CB as missing WARNING: atoms too close: (T0325)T175.CA and (T0325)T175.CB only 0.000 apart, marking (T0325)T175.CB as missing WARNING: atoms too close: (T0325)L180.CA and (T0325)L180.CB only 0.000 apart, marking (T0325)L180.CB as missing WARNING: atoms too close: (T0325)Q182.CA and (T0325)Q182.CB only 0.000 apart, marking (T0325)Q182.CB as missing WARNING: atoms too close: (T0325)F183.CA and (T0325)F183.CB only 0.000 apart, marking (T0325)F183.CB as missing WARNING: atoms too close: (T0325)S189.CA and (T0325)S189.CB only 0.000 apart, marking (T0325)S189.CB as missing WARNING: atoms too close: (T0325)E206.CA and (T0325)E206.CB only 0.000 apart, marking (T0325)E206.CB as missing WARNING: atoms too close: (T0325)F208.CA and (T0325)F208.CB only 0.000 apart, marking (T0325)F208.CB as missing WARNING: atoms too close: (T0325)H213.CA and (T0325)H213.CB only 0.000 apart, marking (T0325)H213.CB as missing WARNING: atoms too close: (T0325)I232.CA and (T0325)I232.CB only 0.000 apart, marking (T0325)I232.CB as missing WARNING: atoms too close: (T0325)E236.CA and (T0325)E236.CB only 0.000 apart, marking (T0325)E236.CB as missing WARNING: atoms too close: (T0325)K244.CA and (T0325)K244.CB only 0.000 apart, marking (T0325)K244.CB as missing WARNING: atoms too close: (T0325)A246.CA and (T0325)A246.CB only 0.000 apart, marking (T0325)A246.CB as missing WARNING: atoms too close: (T0325)R250.CA and (T0325)R250.CB only 0.000 apart, marking (T0325)R250.CB as missing WARNING: atoms too close: (T0325)A255.CA and (T0325)A255.CB only 0.000 apart, marking (T0325)A255.CB as missing WARNING: atoms too close: (T0325)M262.CA and (T0325)M262.CB only 0.000 apart, marking (T0325)M262.CB as missing # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS5 # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 Skipped atom 2, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 4, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 6, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 8, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 10, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 12, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 14, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 16, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 18, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 20, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 22, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 24, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 94, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 96, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 98, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 100, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 102, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 104, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 106, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 108, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 122, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 124, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 126, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 128, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 142, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 144, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 146, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 148, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 170, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 172, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 174, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 176, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 190, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 192, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 194, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 196, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 242, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 244, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 246, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 248, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 250, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 252, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 254, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 256, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 258, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 260, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 262, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 264, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 278, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 280, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 282, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 284, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 286, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 288, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 290, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 292, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 294, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 296, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 298, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 300, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL1 # ReadConformPDB reading from PDB file servers/SAM-T02_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL2 # ReadConformPDB reading from PDB file servers/SAM-T02_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL3 # ReadConformPDB reading from PDB file servers/SAM-T02_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL4 # ReadConformPDB reading from PDB file servers/SAM-T02_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL5 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1 # Found a chain break before 257 # copying to AlignedFragments data structure # naming current conformation SAM_T06_server_TS1 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS2 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS3 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS4 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS5 # ReadConformPDB reading from PDB file servers/SP3_TS1.pdb.gz looking for model 1 # Found a chain break before 228 # copying to AlignedFragments data structure # naming current conformation SP3_TS1 # ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1 # Found a chain break before 223 # copying to AlignedFragments data structure # naming current conformation SP3_TS2 # ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1 # Found a chain break before 155 # copying to AlignedFragments data structure # naming current conformation SP3_TS3 # ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1 # Found a chain break before 208 # copying to AlignedFragments data structure # naming current conformation SP3_TS4 # ReadConformPDB reading from PDB file servers/SP3_TS5.pdb.gz looking for model 1 # Found a chain break before 260 # copying to AlignedFragments data structure # naming current conformation SP3_TS5 # ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1 # Found a chain break before 83 # copying to AlignedFragments data structure # naming current conformation SP4_TS1 # ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1 # Found a chain break before 254 # copying to AlignedFragments data structure # naming current conformation SP4_TS2 # ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1 # Found a chain break before 260 # copying to AlignedFragments data structure # naming current conformation SP4_TS3 # ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1 # Found a chain break before 213 # copying to AlignedFragments data structure # naming current conformation SP4_TS4 # ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1 # Found a chain break before 236 # copying to AlignedFragments data structure # naming current conformation SP4_TS5 # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # Found a chain break before 188 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS1 # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # Found a chain break before 236 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS2 # ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1 # Found a chain break before 241 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS3 # ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1 # Found a chain break before 256 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS4 # ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1 # Found a chain break before 189 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS2 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS3 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS4 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1 WARNING: atoms too close: (T0325)A157.CA and (T0325)D177.CA only 0.000 apart, marking (T0325)D177.CA as missing WARNING: atoms too close: (T0325)S158.CA and (T0325)E178.CA only 0.000 apart, marking (T0325)E178.CA as missing # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation UNI-EID_expm_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL2.pdb.gz looking for model 1 Skipped atom 13, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 14, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 15, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 16, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 25, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 26, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 27, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 28, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 157, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 158, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 159, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 160, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 165, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 166, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 167, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 168, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 193, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 206, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 207, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 208, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 209, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 310, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 311, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 312, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 313, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 314, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 327, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 328, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 329, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 330, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 383, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 384, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 385, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 386, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL2 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL3.pdb.gz looking for model 1 Skipped atom 57, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 170, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 255, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 308, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 313, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 366, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 419, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 420, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 465, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 526, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 675, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 688, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 705, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL3 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL4.pdb.gz looking for model 1 Skipped atom 139, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 152, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 221, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 266, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 311, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 316, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL4 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL5 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1 # Found a chain break before 251 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS1 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS2.pdb.gz looking for model 1 # Found a chain break before 251 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS2 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS3.pdb.gz looking for model 1 # Found a chain break before 256 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS3 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS4.pdb.gz looking for model 1 # Found a chain break before 255 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS4 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS5.pdb.gz looking for model 1 # Found a chain break before 226 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS5 # ReadConformPDB reading from PDB file servers/beautshot_TS1.pdb.gz looking for model 1 # Found a chain break before 260 # copying to AlignedFragments data structure # naming current conformation beautshot_TS1 # ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1 # Found a chain break before 261 # copying to AlignedFragments data structure # naming current conformation beautshotbase_TS1 # ReadConformPDB reading from PDB file servers/forecast-s_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation forecast-s_AL1 # ReadConformPDB reading from PDB file servers/forecast-s_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation forecast-s_AL2 # ReadConformPDB reading from PDB file servers/forecast-s_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation forecast-s_AL3 # ReadConformPDB reading from PDB file servers/forecast-s_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation forecast-s_AL4 # ReadConformPDB reading from PDB file servers/forecast-s_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation forecast-s_AL5 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # Found a chain break before 158 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS2.pdb.gz looking for model 1 # Found a chain break before 169 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS3.pdb.gz looking for model 1 # Found a chain break before 221 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS4.pdb.gz looking for model 1 # Found a chain break before 167 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS5.pdb.gz looking for model 1 # Found a chain break before 256 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS1.pdb.gz looking for model 1 WARNING: atoms too close: (T0325)N9.O and (T0325)A10.N only 0.000 apart, marking (T0325)A10.N as missing # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS2.pdb.gz looking for model 1 WARNING: atoms too close: (T0325)S2.O and (T0325)N3.N only 0.000 apart, marking (T0325)N3.N as missing # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS3.pdb.gz looking for model 1 # Found a chain break before 259 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS4.pdb.gz looking for model 1 WARNING: atoms too close: (T0325)A87.O and (T0325)G88.N only 0.000 apart, marking (T0325)G88.N as missing # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS5.pdb.gz looking for model 1 WARNING: atoms too close: (T0325)T33.O and (T0325)S34.N only 0.000 apart, marking (T0325)S34.N as missing WARNING: atoms too close: (T0325)A87.O and (T0325)G88.N only 0.000 apart, marking (T0325)G88.N as missing # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS5 # ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1 # Found a chain break before 259 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS1 # ReadConformPDB reading from PDB file servers/keasar-server_TS2.pdb.gz looking for model 1 # Found a chain break before 240 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS2 # ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1 # Found a chain break before 232 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS3 # ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1 # Found a chain break before 232 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS4 # ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1 # Found a chain break before 260 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS5 # ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1 WARNING: atom 903 has residue number 1 < previous residue 262 in servers/mGen-3D_TS1.pdb.gz # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation mGen-3D_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation nFOLD_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation nFOLD_TS2 # ReadConformPDB reading from PDB file servers/nFOLD_TS3.pdb.gz looking for model 1 WARNING: atom 1 has residue number 32 < previous residue 262 in servers/nFOLD_TS3.pdb.gz # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation nFOLD_TS3 # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation nFOLD_TS4 # ReadConformPDB reading from PDB file servers/nFOLD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation nFOLD_TS5 # ReadConformPDB reading from PDB file servers/panther2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # naming current conformation panther2_TS1 # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0325 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation shub_TS1 # command:Using radius: 8.0000 Metaserver mode NUMB_ALIGNS: 254 Adding 19999 constraints to all.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all.constraints maxweight: 118.0000 Optimizing... Probability sum: -475.4436, CN propb: -475.4436 weights: 0.2307 constraints: 1286 # command:Found ConstraintSet # PrintContacts align.constraints_meta01 Number of constraints in align.constraints 1286 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta01 Number of constraints in align.constraints.bonus 1286 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta01 Number of constraints in rejected.constraints 18713 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta01 Number of constraints in rejected.constraints.bonus 18713 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_meta01 Number of constraints in noncontact.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_meta01 Number of constraints in noncontact.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_meta01 Number of constraints in all.constraints 19999 # command: